coef: Extract a matrix of model coefficients/standard errors

In DESeq2: Differential gene expression analysis based on the negative binomial distribution

Description

Note: results tables with log2 fold change, p-values, adjusted p-values, etc. for each gene are best generated using the results function. The coef function is designed for advanced users who wish to inspect all model coefficients at once.

Usage

## S3 method for class 'DESeqDataSet'
coef(object, SE = FALSE, ...)

Arguments

object	a DESeqDataSet returned by DESeq, nbinomWaldTest, or nbinomLRT.
SE	whether to give the standard errors instead of coefficients. defaults to FALSE so that the coefficients are given.
...	additional arguments

Details

Estimated model coefficients or estimated standard errors are provided in a matrix form, number of genes by number of parameters, on the log2 scale. The columns correspond to columns of the model matrix for final GLM fitting, i.e., attr(dds, "modelMatrix").

Author(s)

Michael Love

Examples

dds <- makeExampleDESeqDataSet(m=4)
dds <- DESeq(dds)
coef(dds)[1,]
coef(dds, SE=TRUE)[1,]

DESeq2 documentation built on Feb. 22, 2021, 10 a.m.